Open Microscopy Environment

Dear OMERO users and team,

I have some short general questions about OMERO I was not able to
find a satisfying answer to maybe you all can help me out.
I appologize if these have been adresses already and I have overlooked them
Also I will be jumping between different areas of questions.

1. What are the limitations for OMERO in terms of large images?
with large I mean large the range of ~50,000 x 10,000 pixels (in one layer, not stacks)

2. Also is there a way to change the calibration from microns to mm or somethings arbitrary?

3. I was experimenting with images taken with a DSLR in RAW and processed into a JPEG
after importing these into OMERO (running in the vbox) they weren't displayed (rendering engine not ready)
the same jpged image opened in Photoshop and saved again as uncompressed TIFF displayed
fine after import into OMERO. Any hints to why that is?


4. Last questions maybe a bit longer.
what are the exact limitations for OMERO for commercial use.
I was a bit confused as to the use of the GNU license and the existence of this Glenceo company.
Also I already tried to inquiry at Glenceo about a commercial license or additional services but
all the emails bounced (maybe that is fixed now).
Anyway maybe someone can give me a few pointers when OMERO is deployed in a commercial setting.
Is the license needed all the time or can it be used free of charge as long as everything remains open
source?


Sorry again for being all over the place with the questions
but I didn't want to start multiple threads.

Thank you for any pointers.
Cheers
Rob

rkirmse wrote:Dear OMERO users and team,

I have some short general questions about OMERO I was not able to
find a satisfying answer to maybe you all can help me out.
I appologize if these have been adresses already and I have overlooked them
Also I will be jumping between different areas of questions.

1. What are the limitations for OMERO in terms of large images?
with large I mean large the range of ~50,000 x 10,000 pixels (in one layer, not stacks)

There are none. There are some issues in 4.3.x with images with more than 2^31-1 pixels in a single XY plane but they have been resolved for 4.4.0.

rkirmse wrote:2. Also is there a way to change the calibration from microns to mm or somethings arbitrary?

Not at present.

rkirmse wrote:3. I was experimenting with images taken with a DSLR in RAW and processed into a JPEG
after importing these into OMERO (running in the vbox) they weren't displayed (rendering engine not ready)
the same jpged image opened in Photoshop and saved again as uncompressed TIFF displayed
fine after import into OMERO. Any hints to why that is?

RAW and JPEG decode overhead. The images have to be in memory at least twice, if not three times while decompressing and based on the deployment environment you've outlined (running in the vbox) I'd venture to say the memory you have allocated to processes is also insufficient. OMERO deals with ALL data uncompressed, it is not designed to deal with photos.

rkirmse wrote:4. Last questions maybe a bit longer.
what are the exact limitations for OMERO for commercial use.
I was a bit confused as to the use of the GNU license and the existence of this Glenceo company.
Also I already tried to inquiry at Glenceo about a commercial license or additional services but
all the emails bounced (maybe that is fixed now).
Anyway maybe someone can give me a few pointers when OMERO is deployed in a commercial setting.
Is the license needed all the time or can it be used free of charge as long as everything remains open
source?

There are no limitations on OMERO for commercial use as long as the GPL license is adhered to. This basically boils down to if you write applications against OMERO or modify it in any way those applications or changes must also be open source and available under the GPL license. Simply using OMERO for work in a commercial setting without a commercial license is perfectly acceptable and many people do this.

Glencoe Software provides commercial licenses to people who want to (a) receive paid for support or (b) not be constrained by the GPL license. As an example, they may want to write closed source applications against OMERO. PerkinElmer uses this mechanism to distribute OMERO as part of Columbus® (http://www.perkinelmer.com/pages/020/ce ... mbus.xhtml).  

I'm sorry that you had issues contacting Glencoe Software, how did you attempt to do so? I assume that the spelling mistake in the name above "Glenceo" is just an error in this post?

Thank you for all the answer,
that helps a lot.

Regarding the scaling, do you plan to implement a more flexible scaling setup in the future,
maybe similar to "set scale" in imageJ where you can freely define pixelsize and unit name?

I think I had enough RAM allocated for the vbox test environment. It was running with a bit over
4GB of RAM. As I said after converting the JPEG to uncompressed TIFF (~70-80 MB in size) OMERO
displayed these TIFFs fine. But not a big deal I was just curious as to what the source of this Problem
might be and probaby it also solves itself in a "real" production environment where even more
hardware ressources can be allocated.
When you say OMERO is not designed to deal with photos, does that mean monochrome JPEGs are OK
but JPEGs containing RGB channels can be a problem?


Regarding Glencoe (was a typo here) I tried contacting them a while ago through the emails displayed on the website. Maybe the email server was just offline. Anyway it is good to know that they are in operation and available if the need arises.

Thank you again for the help
Best
Rob

Hi,

We have a ticket for specifying units, in particular for pixel sizes: http://trac.openmicroscopy.org.uk/ome/ticket/3741

I'm no expert on the jpeg issues, but I don't imagine there's any difference in the compression between monochrome and RGB jpegs? However I know that monochrome TIFFs are treated as single-channel images, whereas RGB tiffs are split into 3 channels in OMERO, so it's possible the same is true for jpegs?